Ion Reporter Software is a popular option for many Ion Torrent researchers to analyze samples in several different methods(e.g., single-sample analysis comparison against reference, paired analysis between two samples, somatic paired analysis comparing tumor to germline, and inherited trio analysis, comparing proband to parents). Newer functionality includes Copy Number Variation Analysis, Aneuploidy Analysis, as well as utilizing the Ingenuity Variant Analysis Module for extensive annotation capability.
16S metagenomic analysis capability was recently added. Dr. George Watts of the Arizona Cancer Center was profiled in this “Your Innovative Research” article (PDF) where he used V1, V2, and V6 16S rRNA regions along with 200 bp Ion PGMTM system chemistry, and compared its discriminatory power against a single V1-V2 400 bp Ion PGMTM system readlength, and analyzed on Ion ReporterTM Software.
If you are interested in the details about using your custom 16S variable region amplicons with the Ion ReporterTM Software, a document called “Ion 16S™ Software Steps for Custom Primers” has been uploaded to the Ion Community website. If you are just curious about what the Ion ReporterTM Software interface looks like, simply register a new account on Ion ReporterTM here. A mock 16S dataset has already been uploaded for you.
In case you have been looking at that 16S mock dataset and your local computational biologist starts asking questions about filters, JSON files, and blastn settings, you can point them to this document: “Metagenomics 16S Algorithms Overview” also on Ion Community. The document explains ‘under the hood’ details. (There are 18 pages of detail, in fact.) It is written to help experienced bioinformatic specialists to compare their findings with previously generated data, as well as information on parameters to adjust for stringency as well as explaining usage of the curated database content.
If you’d like to see what Dr. David Visi (Baylor College of Medicine, Houston Texas) is doing with 16S metagenomic analysis on the Ion PGMTM system, watch this quick video analyzing the microbial retting community of kenaf, an economically valuable fiber.